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Old 11-27-2011, 08:26 AM   #1
CS Student
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Default Error in Compiling BFAST

Hi,

I am trying to compile the source code of BFAST and I am getting the below error message when trying to "make". Appreciate any advice on the error message.

* I use "./configure" before "make".

Thanks
=====================
make all-recursive
make[1]: Entering directory `/hadoop/bfast-filesí
Making all in bfast
make[2]: Entering directory `/hadoop/bfast-filesí
gcc -Wall -g -O2 -pthread -o bfast AlignedEnd.o AlignedEntry.o AlignedRead.o AlignedReadConvert.o BError.o BLib.o RGBinary.o RGIndex.o RGIndexAccuracy.o RGIndexExons.o RGIndexLayout.o RGMatch.o RGMatches.o RGRanges.o RGReads.o ScoringMatrix.o Align.o AlignNTSpace.o AlignColorSpace.o AlignMatrix.o MatchesReadInputFiles.o RunMatch.o RunLocalAlign.o RunPostProcess.o RunAlign.o BfastFasta2BRG.o BfastIndex.o BfastMatch.o BfastLocalAlign.o BfastPostProcess.o BfastBAFConvert.o BfastHeader.o BfastBMFConvert.o BfastBRG2Fasta.o BfastAlign.o aflib.o Main.o -lm -lbz2 -lz
AlignedEnd.o: file not recognized: File format not recognized
collect2: ld returned 1 exit status
make[2]: *** [bfast] Error 1
make[2]: Leaving directory `/hadoop/bfast-filesí
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/hadoop/bfast-filesí
make: *** [all] Error 2
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Old 11-27-2011, 08:30 PM   #2
nilshomer
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Could you try"./configure && make clean && make" and post all output?
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Old 11-27-2011, 10:22 PM   #3
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It works fine now using "make clean" before "make".

Thanks a lot Nils!
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Old 04-17-2012, 02:54 PM   #4
peas1127
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I am having similar problem but solution didn't work for me here is what i did


sh autogen.sh
./configure
then make

i get this error:


make all-recursive
make[1]: Entering directory `/directory/BFAST/bfast-0.7.0a'
Making all in bfast
make[2]: Entering directory `/directory/BFAST/bfast-0.7.0a/bfast'
depbase=`echo BLib.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -Wall -g -O2 -pthread -MT BLib.o -MD -MP -MF "$depbase.Tpo" -c -o BLib.o BLib.c; \
then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi
BLib.c: In function 'OpenTmpFile':
BLib.c:480: error: 'ZLIB_VERNUM' undeclared (first use in this function)
BLib.c:480: error: (Each undeclared identifier is reported only once
BLib.c:480: error: for each function it appears in.)
BLib.c: In function 'OpenTmpGZFile':
BLib.c:553: error: 'ZLIB_VERNUM' undeclared (first use in this function)
make[2]: *** [BLib.o] Error 1
make[2]: Leaving directory `/directory/BFAST/bfast-0.7.0a/bfast'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/directory/BFAST/bfast-0.7.0a'
make: *** [all] Error 2

i tried make clean but it still gave me this:

make all-recursive
make[1]: Entering directory `/directory/BFAST/bfast-0.7.0a'
Making all in bfast
make[2]: Entering directory `/directory/BFAST/bfast-0.7.0a/bfast'
depbase=`echo AlignedEnd.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -Wall -g -O2 -pthread -MT AlignedEnd.o -MD -MP -MF "$depbase.Tpo" -c -o AlignedEnd.o AlignedEnd.c; \
then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi
depbase=`echo AlignedEntry.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -Wall -g -O2 -pthread -MT AlignedEntry.o -MD -MP -MF "$depbase.Tpo" -c -o AlignedEntry.o AlignedEntry.c; \
then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi
depbase=`echo AlignedRead.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -Wall -g -O2 -pthread -MT AlignedRead.o -MD -MP -MF "$depbase.Tpo" -c -o AlignedRead.o AlignedRead.c; \
then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi
depbase=`echo AlignedReadConvert.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -Wall -g -O2 -pthread -MT AlignedReadConvert.o -MD -MP -MF "$depbase.Tpo" -c -o AlignedReadConvert.o AlignedReadConvert.c; \
then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi
depbase=`echo BError.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -Wall -g -O2 -pthread -MT BError.o -MD -MP -MF "$depbase.Tpo" -c -o BError.o BError.c; \
then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi
depbase=`echo BLib.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \
if gcc -DHAVE_CONFIG_H -I. -I. -I.. -Wall -g -O2 -pthread -MT BLib.o -MD -MP -MF "$depbase.Tpo" -c -o BLib.o BLib.c; \
then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi
BLib.c: In function 'OpenTmpFile':
BLib.c:480: error: 'ZLIB_VERNUM' undeclared (first use in this function)
BLib.c:480: error: (Each undeclared identifier is reported only once
BLib.c:480: error: for each function it appears in.)
BLib.c: In function 'OpenTmpGZFile':
BLib.c:553: error: 'ZLIB_VERNUM' undeclared (first use in this function)
make[2]: *** [BLib.o] Error 1
make[2]: Leaving directory `/directory/BFAST/bfast-0.7.0a/bfast'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/directory/BFAST/bfast-0.7.0a'
make: *** [all] Error 2


can someone please help me.?
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